R/ApplyGate.R

In Mthrun/dbt.FlowCytometry: Databionics Toolbox for the Analysis of Fluorescence-Activated Cell Sorting (FACS) Data

ApplyGate=function(Data,GateVar1,GateVar2,Polygon,PlotIt=FALSE,PlotSampleSize=1000){
#V= ApplyGate(Data, GateVar1, GateVar2, Polygon, PlotIt = FALSE, PlotSampleSize = 1000)
#A specific Gate defined by xy coordinates that result in a closed polygon is applied to the flowcytometry data.
#
# INPUT
# Data                numerical matrix n x d
# GateVar1            either column index in Data of X coordinate of gate or variable name as string if matrix has named cols.
# GateVar2            either column index in Data of Y coordinate of gate or variable name as string if matrix has named cols.
# Polygon             numerical marix of two columns defining the coordiantes of the polygon, polygon has to be closed, i.e., first and last coordinate has to be the same
# PlotIt              if TRUE: plots a sample of data in the two selected variables and marks point inside the gate as yellow and outside as magenta
# PlotSampleSize      size of the plottet sample
#
#OUTPUT
#   list of
# DataInGate        m x d numerical matrix with m<=n of data points inside the gate
# InGateInd         index of length m for the datapoints in original matrix

#DETAILS
# Gates are alwaxs two dimensional, i.e., require two filters, although all dimensions of data are filted by the gates. Only high-dimensional points inside the polygon (gate) are given back
#   if GateVar1 or GateVar2 is not found a text is given back which will state this issue

#   Michael Thrun
#EXAMPLE
  #   Data <- matrix(runif(1000), ncol = 10)
  #   colnames(Data)=paste0("GateVar",1:ncol(Data))
  #   poly <- cbind(x = c(0.2,0.5,0.8), y = c(0.2,0.8,0.2))
  #   #set plotit TRUE for understanding the example
  #   V=ApplyGate(Data,"GateVar5","GateVar8",poly,PlotIt=F,100)
  #   V=ApplyGate(Data,5,8,poly,PlotIt=F,100)

 if(!is.numeric(GateVar1) & !is.numeric(GateVar2)){
   if(is.null(colnames(Data))){
     text="One or two of the Gate variables not found in data, because strings are used for 'GateVar1'/'GateVar1' but 'Data' has no column names. Please provide column indices instead or name columns of data."
     message(text)
     return(text)
   }
 }

  X=Data[,GateVar1]
  Y=Data[,GateVar2]

  GateData=cbind(X,Y)

  if(dim(GateData)[2]){
    InGateCls=ScatterDensity::PointsInPolygon(GateData,Polygon = Polygon,PlotIt = F)
    ind=which(InGateCls==2)
    DataInGate=Data[ind,]
    if(isTRUE(PlotIt)){
      GateDataSample=GateData[sample(1:nrow(GateData),replace = T,size = PlotSampleSize),]
      if(is.numeric(GateVar1))
        xlab=paste("Index",GateVar1,"specifying Variable", colnames(Data)[GateVar1])
      else
        xlab=GateVar1

      if(is.numeric(GateVar2))
        ylab=paste("Index",GateVar2,"specifying Variable", colnames(Data)[GateVar2])
      else
        ylab=GateVar2

      XYlab=colnames(GateDataSample)
      ScatterDensity::PointsInPolygon(GateDataSample,Polygon = Polygon,
                                                 PlotIt = T,main = "Yellow = In Gate",xlab=xlab,ylab=ylab)
    }
    return(list(DataInGate=DataInGate,InGateInd=ind))
  }else{
    text="One or two of the Gate variables not found in data. Please check manually"
    message(text)
    return(text)
  }


}